Simulation of FUS Protein Condensates with an Adapted Coarse-Grained Model

Protein secondary-structure description with a coarse-grained model.

A coarse-grained geometrical model for protein secondary-structure description and analysis is presented which uses only the positions of the C(α) atoms. A space curve connecting these positions by piecewise polynomial interpolation is constructed and the folding of the protein backbone is described by a succession of screw motions linking the Frenet frames at consecutive C(α) positions. Using ...

Protein secondary structure analysis with a coarse-grained model

The paper presents a geometrical model for protein secondary structure analysis which uses only the positions of the Cα-atoms. We construct a space curve connecting these positions by piecewise polynomial interpolation and describe the folding of the protein backbone by a succession of screw motions linking the Frenet frames at consecutive Cα-positions. Using the ASTRAL subset of the SCOPe data...

Coarse - Grained Refractory Inclusions : Condensates , Evaporation Residues , or Both ?

Coarse-grained simulation of polymer translocation through an artificial nanopore

The translocation of a macromolecule through a nanometer-sized pore is an interesting process with important applications in the development of biosensors for single–molecule analysis and in drug delivery and gene therapy. We have carried out a molecular dynamics simulation study of electrophoretic translocation of a charged polymer through an artificial nanopore to explore the feasibility of s...

Coarse-Grained Simulation of DNA using LAMMPS

During the last decade coarse-grained nucleotide models have emerged that allow us to DNA and RNA on unprecedented time and length scales. Among them is oxDNA, a coarse-grained, sequence-specific model that captures the hybridisation transition of DNA and many structural properties of singleand double-stranded DNA. oxDNA was previously only available as standalone software, but has now been imp...